I'll have to dig the picture of the settings (I'm not home right now).
They're not the same as I use for live so it's hard to tell.
But I do know I always run treble very high (9-10) and bass almost off, mid around 3 depending on the guitar.
I like the run the presence fairly high and go easy on the last slider on the EQ.
One particular thing I do in studio is tweak the amp with isolation headphones on.
Basically I set the amp to something I like, then I strap on the headphones and move the mic until I find the tone I'm looking for and then re-tweak the amp from there (without looking, just by listening!).
Usually, by the time I like what I hear in my headphones (which is what gets recorded), what I hear when I remove them doesn't sound so good. I'm really concentrating on what gets recorded.
The SM57 on a G12T-75 speaker (plus the high presence setting) might account for the more agressive sound, but I'd say it's mostly the very high treble setting and the use of ceramic pickups (Gibson 500T).
And since doing this recording (which was just released, but was really recorded 8 months ago), I've came to the conclusion that a Sennheiser MD421 on a Rectifier cab is the best match for a Mark IV.
Actually, Petrucci does just that (mixed with a SM57).
I did some clips for fun using this micing combo and the R2 channel and you wouldn't believe it's R2! The tone is similar to Metallica's Load. I hope I still have it somewhere.
Thanks for the comments.